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(-) Description

Title :  CRYSTAL STRUCTURE OF DNA-BINDING DOMAIN OF BACILLUS SUBTILIS YYCF
 
Authors :  T. Okajima, A. Okada, T. Watanabe, K. Yamamoto, K. Tanizawa, R. Utsumi
Date :  01 Sep 05  (Deposition) - 12 Sep 06  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Helix-Turn-Helix Motif, Dna-Binding Domain, Two-Component System, Response Regulator, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Okajima, A. Doi, A. Okada, Y. Gotoh, K. Tanizawa, R. Utsumi
Response Regulator Yycf Essential For Bacterial Growth: X-Ray Crystal Structure Of The Dna-Binding Domain And Its Phob-Like Dna Recognition Motif
Febs Lett. V. 582 3434 2008
PubMed-ID: 18789936  |  Reference-DOI: 10.1016/J.FEBSLET.2008.09.007
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATORY PROTEIN YYCF
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN (RESIDUES 128-235)
    Gene: YYCF
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2D1V)

(-) Sites  (0, 0)

(no "Site" information available for 2D1V)

(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OMPR_PHOBPS51755 OmpR/PhoB-type DNA-binding domain profile.WALR_BACSU132-231  1A:132-231

(-) Exons   (0, 0)

(no "Exon" information available for 2D1V)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:103
 aligned with WALR_BACSU | P37478 from UniProtKB/Swiss-Prot  Length:235

    Alignment length:103
                                   140       150       160       170       180       190       200       210       220       230   
           WALR_BACSU   131 SSNEIHIGSLVIFPDAYVVSKRDETIELTHREFELLHYLAKHIGQVMTREHLLQTVWGYDYFGDVRTVDVTVRRLREKIEDNPSHPNWIVTRRGVGYYLRNPE 233
               SCOP domains d2d1va_ A: automated matches                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeee....eeee..ee...hhhhhhhhhhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhhhhhh........eeee...eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -OMPR_PHOB  PDB: A:132-231 UniProt: 132-231                                                          -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2d1v A 131 SSNEIHIGSLVIFPDAYVVSKRDETIELTHREFELLHYLAKHIGQVMTREHLLQTVWGYDYFGDVRTVDVTVRRLREKIEDNPSHPNWIVTRRGVGYYLRNPE 233
                                   140       150       160       170       180       190       200       210       220       230
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D1V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D1V)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (WALR_BACSU | P37478)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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UniProtKB/Swiss-Prot
        WALR_BACSU | P37478: 2zwm 3f6p

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